The origin of photosynthesis and the evolution of photosynthetic diversity are major topics that are tied closely to the evolution of all life on Earth either through phylogenetics or indirectly through the evolution of planetary conditions. Chloroflexus aurantiacus is important in studies addressing these topics.

Cfl. aurantiacus is an intriguing anoxygenic phototroph. Its intrigue became evident when its isolation and initial characterization led to the description of a phototroph that has characteristics typical of both the green sulfur bacteria and the purple bacteria. Its chimeric character fueled speculation that it might be some remnant of an ancient lineage of phototrophs. Sequence of its small subunit rRNA confirmed that its place on the tree of life was in the earliest branch that contained phototrophs, somewhat distant from the other phototrophs. Lateral gene transfer, however, has blurred the evolutionary history of photosynthetic prokaryotes.

Cfl. aurantiacus is a filamentous gliding phototroph. It is a thermophile forming massive accumulations as conspicuous mats in neutral to alkaline hot springs. Chloroflexus is found at higher temperatures than any other anoxygenic phototroph. Its optimal growth temperature lies between 50 and 60çC in laboratory cultures. It is typically found as the lower layer of a microbial mat with cyanobacteria growing in layers above it. In springs high in sulfide, however, Chloroflexus may be found alone.

Chloroflexus grows primarily as a photoheterotroph and appears to consume the organic products of the autotrophic cyanobacteria in its native habitat. Some strains can grow autotrophically, however, using hydrogen or sulfide as an electron donor. The CO2 fixation mechanism, the 3-hydroxypropionate pathway, is unique among all phototrophs. Cells appear to lack ribulose bisphosphate carboxylase activity. The light-harvesting apparatus consists of chlorosomes appressed to the cell membrane. The chlorosomes are somewhat smaller that those of the green sulfur bacteria. The chlorosomes contain the accessory bacteriochlorophyll c. Light-harvesting complexes containing Bchl a similar to those of the purple bacteria are located in the cell membrane. The pheophytin-quinone type photochemical reaction centers are also similar to those of the purple bacteria. The cells, however, lack internal membranes typical of the purple bacteria.

Cfl. aurantiacus is found along with several related anoxygenic filamentous phototrophs in the green non-sulfur bacterial (GNSB) branch of the 16S rRNA tree of life. The name of this branch is an unfortunate descriptor because it suggests that all members are green and do not use sulfide, both of which are not true. The diversity of the Chloroflexus relatives contributes to the intrigue about the origins and evolution of photosynthesis. Another species of Chloroflexus, has recently been described, Cfl. aggregans, which is also found in hot spring mats. More distantly related is the recently described freshwater mesophile, Oscillochloris trichoides. O. trichoides is a gliding filament, but differs from Chloroflexus in habitat, being found in sulfide-containing sediments in springs and lakes. It also differs from Chloroflexus by fixing CO2 with ribulose bisphosphate carboxylase via the Calvin cycle. Marine Chloroflexus-like organisms have also been described from marine and hypersaline microbial mats. The planktonic Chloronema is found in the anoxic zones of freshwater lakes. Perhaps most striking, however, is the presence of at least two species of "red" filamentous phototrophs in this branch that lack chlorosomes and contain only bacteriochlorophyll a. Heliothrix oregonensis and "Roseiflexus castenholzii" have been found in hot springs along with Chloroflexus.

Cfl. aurantiacus is the most thoroughly studied member of the GNSB lineage. This branch contains the diverse group of phototrophs described above that cluster together distinct from the non-photosynthetic members of the group. Understanding the evolution of photosynthesis within this group and the evolution of photosynthesis among all phototrophs is dependent on genomics. The sequence of the genome of Chloroflexus will help to answer relevant questions.